Merge pull request #138 from eScienceLab/typo-fixes

kikkomep · web-flow · commit 35039a19cf67 · 2026-01-07T11:07:10.000+01:00
Fix typos; add `typos` package to CI
diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -25,9 +25,9 @@ env:
     FORCE_COLOR: "1"  # Force color output in CI
 
 jobs:
-    # Verifies pep8, pyflakes and circular complexity
-    flake8:
-        name: 🚨 Lint Python Code
+    # Verifies pep8, pyflakes, circular complexity, and spelling
+    lint:
+        name: 🚨 Lint and spellcheck
         runs-on: ubuntu-latest
         steps:
             # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
@@ -39,14 +39,16 @@ jobs:
                   python-version: ${{ env.PYTHON_VERSION }}
             - name: 🔽 Install flake8
               run: pip install flake8
-            - name: ⌛ Run checks
+            - name: ⌛ Lint Python code
               run: flake8 -v rocrate_validator tests
+            - name: ⌛ Spell check code and profiles (covers Python and SHACL)
+              uses: crate-ci/typos@v1.41.0
 
     # Runs the tests
     test:
         name: ⌛ Run tests
         runs-on: ubuntu-latest
-        needs: [flake8]
+        needs: [lint]
         steps:
             - name: ⬇️ Checkout
               uses: actions/checkout@v4
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -70,6 +70,7 @@ requests = ">=2.32,<3.0"
 requests-cache = ">=1.2,<2.0"
 inquirerpy = ">=0.3.4,<0.4.0"
 enum-tools = ">=0.12,<0.13"
+typos = "^1.41.0"
 
 [tool.poetry.group.dev.dependencies]
 pyproject-flake8 = "^6.1.0"
@@ -105,3 +106,6 @@ skip_dirs = [".git", ".github", ".vscode"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+
+[tool.typos.files]
+extend-exclude = ["tests/data","docs/diagrams","*.json","*.html","*__init__.py"]
diff --git a/rocrate_validator/profiles/process-run-crate/profile.ttl b/rocrate_validator/profiles/process-run-crate/profile.ttl
@@ -44,7 +44,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -62,7 +62,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"
diff --git a/rocrate_validator/profiles/provenance-run-crate/profile.ttl b/rocrate_validator/profiles/provenance-run-crate/profile.ttl
@@ -45,7 +45,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -63,7 +63,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"
diff --git a/rocrate_validator/profiles/provenance-run-crate/should/5_parameterconnection.ttl b/rocrate_validator/profiles/provenance-run-crate/should/5_parameterconnection.ttl
@@ -29,7 +29,7 @@ provenance-run-crate:ProvRCParameterConnectionReferencesRecommended a sh:NodeSha
     sh:description "Recommended references for ParameterConnection entities" ;
     sh:targetClass wfrun:ParameterConnection ;
     sh:property [
-        sh:name "ParamenterConnection references" ;
+        sh:name "ParameterConnection references" ;
         sh:description """References to `ParameterConnection` instances
         SHOULD follow the CWL convention,
         where connections to workflow output parameters are referenced by the workflow
diff --git a/rocrate_validator/profiles/ro-crate/may/4_data_entity_metadata.ttl b/rocrate_validator/profiles/ro-crate/may/4_data_entity_metadata.ttl
@@ -27,7 +27,7 @@ ro-crate:FileDataEntityWebOptionalProperties a sh:NodeShape ;
     for instance a landing page that describes the file, including persistence identifiers (e.g. DOI),
     resolving to an intermediate HTML page instead of the downloadable file directly.
     These can included for File Data Entities as additional metadata by using the properties:
-    `ìdentifier`, `url`, `subjectOf`and `mainEntityOfPage`""" ;
+    `identifier`, `url`, `subjectOf`and `mainEntityOfPage`""" ;
     sh:targetClass ro-crate:File ;
     # Check if the Web-based Data Entity has a contentSize property
     sh:property [
@@ -87,4 +87,3 @@ ro-crate:DirectoryDataEntityWebOptionalDistribution a sh:NodeShape ;
         sh:severity sh:Info ;
         sh:message """The Directory Data Entity MAY have a `distribution` property to denote the distribution of the files within the directory""" ;
     ] .
-
diff --git a/rocrate_validator/profiles/ro-crate/must/2_root_data_entity_metadata.ttl b/rocrate_validator/profiles/ro-crate/must/2_root_data_entity_metadata.ttl
@@ -129,7 +129,7 @@ ro-crate:RootDataEntityRequiredProperties
     ] ;
     sh:property [
         a sh:PropertyShape ;
-        sh:name "Root Data Entity: `licence` property" ;
+        sh:name "Root Data Entity: `license` property" ;
         sh:description """Check if the Root Data Entity includes a `license` property (as specified by schema.org)
         to provide information about the license of the dataset.""" ;
         sh:path schema_org:license;
diff --git a/rocrate_validator/profiles/ro-crate/must/4_data_entity_metadata.ttl b/rocrate_validator/profiles/ro-crate/must/4_data_entity_metadata.ttl
@@ -23,7 +23,7 @@
 ro-crate:DataEntityRequiredProperties a sh:NodeShape ;
     sh:name "Data Entity: REQUIRED properties" ;
     sh:description """A Data Entity MUST be a `URI Path` relative to the ROCrate root,
-        or an sbsolute URI""" ;
+        or an absolute URI""" ;
     sh:targetClass ro-crate:DataEntity ;
 
     sh:property [
@@ -130,9 +130,9 @@ ro-crate:DirectoryDataEntity a sh:NodeShape ;
         sh:severity sh:Violation ;
     ] .
 
-ro-crate:DataEntityRquiredPropertiesShape a sh:NodeShape ;
+ro-crate:DataEntityRequiredPropertiesShape a sh:NodeShape ;
     sh:name "Data Entity: REQUIRED properties" ;
-    sh:description """A `DataEntity` MUST be linked, either directly or inderectly, from the Root Data Entity""" ;
+    sh:description """A `DataEntity` MUST be linked, either directly or indirectly, from the Root Data Entity""" ;
     sh:targetClass ro-crate:DataEntity ;
     sh:property
         [
@@ -141,7 +141,7 @@ ro-crate:DataEntityRquiredPropertiesShape a sh:NodeShape ;
             sh:node schema_org:Dataset ;
             sh:minCount 1 ;
             sh:name "Data Entity MUST be directly referenced" ;
-            sh:description """Check if the Data Entity is linked, either directly of inderectly, to the `Root Data Entity` using the `hasPart` (as defined in `schema.org`) property" """ ;
+            sh:description """Check if the Data Entity is linked, either directly or indirectly, to the `Root Data Entity` using the `hasPart` (as defined in `schema.org`) property" """ ;
             # sh:message "A Data Entity MUST be directly or indirectly linked to the `Root Data Entity` through the `hasPart` property" ;
         ] .
 
diff --git a/rocrate_validator/profiles/ro-crate/must/6_contextual_entity.ttl b/rocrate_validator/profiles/ro-crate/must/6_contextual_entity.ttl
@@ -24,7 +24,7 @@
 
 ro-crate:FindLicenseEntity a sh:NodeShape, validator:HiddenShape ;
     sh:name "Identify License Entity" ;
-    sh:description """Mark a license entity any Data Entity referenced by the `schema:licence` property.""" ;
+    sh:description """Mark a license entity any Data Entity referenced by the `schema:license` property.""" ;
     sh:target [
         a sh:SPARQLTarget ;
         sh:prefixes ro-crate:sparqlPrefixes ;
@@ -68,7 +68,7 @@ ro-crate:WebSiteRecommendedProperties a sh:NodeShape ;
 
 ro-crate:CreativeWorkAuthorDefinition a sh:NodeShape, validator:HiddenShape ;
     sh:name "CreativeWork Author Definition" ;
-    sh:description """Define the `CretiveWorkAuthor` as the `Person` object of the `schema:author` predicate.""" ;
+    sh:description """Define the `CreativeWorkAuthor` as the `Person` object of the `schema:author` predicate.""" ;
     sh:targetObjectsOf schema:author ;
     sh:rule [
         a sh:TripleRule ;
@@ -79,4 +79,3 @@ ro-crate:CreativeWorkAuthorDefinition a sh:NodeShape, validator:HiddenShape ;
             sh:property [ sh:path rdf:type ; sh:hasValue schema:Person ; sh:minCount 1 ] ;
         ] ;
     ] .
-
diff --git a/rocrate_validator/profiles/ro-crate/profile.ttl b/rocrate_validator/profiles/ro-crate/profile.ttl
@@ -40,7 +40,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -58,7 +58,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"
diff --git a/rocrate_validator/profiles/ro-crate/should/2_root_data_entity_metadata.ttl b/rocrate_validator/profiles/ro-crate/should/2_root_data_entity_metadata.ttl
@@ -27,7 +27,7 @@ ro-crate:RootDataEntityDirectRecommendedProperties a sh:NodeShape ;
     sh:targetClass ro-crate:RootDataEntity ;
     sh:property [
         a sh:PropertyShape ;
-        sh:name "Root Data Entity: `licence` SHOULD link to a Contextual Entity" ;
+        sh:name "Root Data Entity: `license` SHOULD link to a Contextual Entity" ;
         sh:description """Check if the Root Data Entity includes a `license` property 
         that links to a Contextual Entity with type `schema_org:CreativeWork` to describe the license.""" ;
         sh:nodeKind sh:BlankNodeOrIRI ;
diff --git a/rocrate_validator/profiles/ro-crate/should/6_contextual_entity_metadata.ttl b/rocrate_validator/profiles/ro-crate/should/6_contextual_entity_metadata.ttl
@@ -18,7 +18,7 @@
 @prefix sh: <http://www.w3.org/ns/shacl#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
-ro-crate:CreativeWorkAuthorMinimuRecommendedProperties a sh:NodeShape ;
+ro-crate:CreativeWorkAuthorMinimumRecommendedProperties a sh:NodeShape ;
     sh:name "CreativeWork Author: minimum RECOMMENDED properties" ;
     sh:description """The minimum recommended properties for a `CreativeWork Author` are `name` and `affiliation`.""" ;
     sh:targetClass ro-crate:CreativeWorkAuthor ;
diff --git a/rocrate_validator/profiles/workflow-ro-crate/must/0_main-workflow.ttl b/rocrate_validator/profiles/workflow-ro-crate/must/0_main-workflow.ttl
@@ -21,7 +21,7 @@
 @prefix sh: <http://www.w3.org/ns/shacl#> .
 @prefix validator: <https://github.com/crs4/rocrate-validator/> .
 
-workflow-ro-crate:MainEntityProperyMustExist a sh:NodeShape ;
+workflow-ro-crate:MainEntityPropertyMustExist a sh:NodeShape ;
     sh:name "Main Workflow entity existence" ;
     sh:description "The Main Workflow must be specified through a `mainEntity` property in the root data entity" ;
     sh:targetClass ro-crate:RootDataEntity ;
@@ -63,13 +63,13 @@ workflow-ro-crate:MainWorkflowRequiredProperties a sh:NodeShape ;
     sh:property [
         a sh:PropertyShape ;
         sh:name "Main Workflow type" ;
-        sh:description "The Main Workflow must have types File, SoftwareSourceCode, ComputationalWorfklow" ;
+        sh:description "The Main Workflow must have types File, SoftwareSourceCode, ComputationalWorkflow" ;
         sh:path rdf:type ;
         sh:hasValue schema:MediaObject ,
                     schema:SoftwareSourceCode ,
                     bioschemas:ComputationalWorkflow ;
         sh:minCount 1 ;
-        sh:message "The Main Workflow must have types File, SoftwareSourceCode, ComputationalWorfklow" ;
+        sh:message "The Main Workflow must have types File, SoftwareSourceCode, ComputationalWorkflow" ;
     ] ;
     sh:property [
         a sh:PropertyShape ;
diff --git a/rocrate_validator/profiles/workflow-ro-crate/profile.ttl b/rocrate_validator/profiles/workflow-ro-crate/profile.ttl
@@ -44,7 +44,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -62,7 +62,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"
diff --git a/rocrate_validator/profiles/workflow-run-crate/profile.ttl b/rocrate_validator/profiles/workflow-run-crate/profile.ttl
@@ -45,7 +45,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -63,7 +63,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"
diff --git a/rocrate_validator/profiles/workflow-testing-ro-crate/profile.ttl b/rocrate_validator/profiles/workflow-testing-ro-crate/profile.ttl
@@ -43,7 +43,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -61,7 +61,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"
diff --git a/rocrate_validator/rocv_io/output/text/formatters.py b/rocrate_validator/rocv_io/output/text/formatters.py
@@ -42,7 +42,7 @@ def __rich_console__(self, console: Console, options: ConsoleOptions) -> RenderR
 
         # Print validation details
         # Print the list of failed requirements
-        yield Padding("\n[bold]The following requirements have not meet: [/bold]", (0, 2))
+        yield Padding("\n[bold]The following requirements have not been met: [/bold]", (0, 2))
         for requirement in sorted(result.failed_requirements, key=lambda x: x.identifier):
             yield Align(f"\n[profile: [magenta bold]{requirement.profile.name}[/magenta bold]]", align="right")
 
diff --git a/tests/integration/profiles/workflow-ro-crate/test_main_workflow.py b/tests/integration/profiles/workflow-ro-crate/test_main_workflow.py
@@ -31,7 +31,7 @@ def test_main_workflow_bad_type():
         Severity.REQUIRED,
         False,
         ["Main Workflow definition"],
-        ["The Main Workflow must have types File, SoftwareSourceCode, ComputationalWorfklow"],
+        ["The Main Workflow must have types File, SoftwareSourceCode, ComputationalWorkflow"],
         profile_identifier="workflow-ro-crate"
     )
 
